Welcome aboard. Sure, those don't sound particularly difficult. It's been a while though and I don't have the game installed right now.

1. Mercs are definitely defined in one of the xml files, a quick look through them would likely point you in the right direction. Their ships may possibly be in Carcasses.xml just like all the rest though, and the layouts in that other file. The other modders can help you out here, I didn't touch them much.

2. Custom pilot, sure. Getting the script to let him tag along from the start, theoretically should be possible. Goblin Wizard can advise you better since he worked on pilots a lot.

3. Definitely, the logos are stashed somewhere in the textures subfolders. Should be no problem just replacing them. Ditto the pilots. Their icons would be a little trickier since they're also stuffed in a few other files, some containing all of them together (the map overlay ones iirc). If you trawl through the textures folder though it's likely you'll find them.

4. Those should all be in each system's script, just need to edit them. Comparing Nanaki's with the originals should help.

5. Theoretically just need to remove the mission script triggers after that one. Still, during the free time parts you can actually ignore the story and go wherever you want as long as you don't reach the target station iirc.

6. Should be easy, just replace the ship model and definitions.

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The game has a few script bugs - all which we've fixed iirc. I don't particularly remember that mission but try see if downloading the fixed scripts help, the thread should be in here somewhere.

Good luck.